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When I brunt WAV into audio CD, it is no longer a WAV. Compare to original WAV files, those cda files in CD-R sound better with more depth in field. Those instruments sound more crisp, more precise. The vocal stands out further from those instruments, reaching closer to you where those vocal accompaniment still stays behind. Seriously i don't know how to put those "better how" in words. My english is not better than my ear
AFAIK .cda files do not contain audio data in the CD media, just start and end indexes (
http://www.wisegeek.com/what-is-a-cda-file.htm)
Also, binary information written to a CD is not of the 1's and 0's form if you want to go down the path of details. Each CD vendor recommends a different "write strategy." This is vendor media and writing speed dependent. The strategy dictates the laser power used, and it can be different depending on the number of consecutive 1's and 0's. If I remember correctly, I think the 1's and 0's are run length encoded before being written. Not all burners support all "write strategies"/write speeds. Newer ones have a better chance at multiple support. This is not just something I read out of wikipedia, I briefly worked on this crap some years ago (laser driver control) but I'm not current on it (working on some other crap right now.) Reading is easier because if I remember correctly, a constant (and lower) laser power is needed, but the power might vary from CD type and vendor-to-vendor... Again, I can't remember all the details.
The signal processor of a CD player - which may be a fairly elaborate full receiver with adaptive equalization and powerful error correction schemes (sold and ridiculously low amounts of $ due to volume sales and competition) - will recover PCM digital 1's and 0's. I think SIMILAR could be said about reading a magnetic Harddrive.
Either way, the PCM stream resulting from reading your CD player and your HD (which I think - don't remember well - also uses run length encoding, equalization, precise timing, error correction and so on stuff) should look identical when presented to the same DAC... Assuming your computer doesn't do some magical Mickey-soft driver dependent stuff... Like my HP laptop craptastic Beats (the crap out of my) audio, which I have a hard time turning off.
You are also describing differences that are typically a result of mastering, digital signal path equalization, and analog/acoustic signal path coloration... and equailzation. All of which do not get impacted by the storage format... at all AFAIK.
If you hear these differences, more power to you, but my 2 cents here are that I have not heard these differences you are describing between my ripped files and my original music CDs (and DVD/BR movies) when megacrap drivers don't get in the way. Nor can I explain why in particular you might be perceiving an improvement in sound quality when using a CD-R file vs. an HD file. But I may just be overlooking something... Dunno.
(EDIT: CDs are not run length coded, but run length limited coded... like I said, it's been some time.)